Marvel: Ultimate Alliance (Wii)
(October 24, 2006)
The only source for this information is the official site of Jason Harlow, a senior artist from Vicarious Visions, the company that developed this version of the game. In his site he posted animations of the two characters in battle. For some reason, though, the animations were later removed, as were references to the game in Link's images, which were then labeled "Personal project". (found here:)
While created pureposelly for the Wii version, it seems that Link and Samus were removed from the game on Nintendo's request. Another oddity is that Jason Harlow removed from his site any evidence of Link and Samus ever being intended to appear in the game. This likely has to do with bad publicity that would go to the game from showing features not in the final version.